I am facing similar problem, but almost sure it is OS related.
My system here is a Win 7 64bits, I downloaded the latest drivers and software from NI site. I am using a VB6 pro edition. In this system, the serial poll query is not working properly for any equipment. Sometimes after performing a serial poll, where the status byte indicates that the MAV bit is set, the following command is ibread to the instrument which returns an empty string or simply times out. If I do not perform the serial poll, the ibread command returns string as expected. I checked and enabled the bits with *SRE accordingly, even this command sometimes hungs when sent to the equipment. If I go to a Win XP 32 bits, the program runs properly.
Are you using the same GPIB devices on both systems? Have you also checked in Measurement & Automation Explorer to see if the GPIB controller's settings are identical between the 2 machines? Specifically make sure that the autopolling settings match on both systems.
Justin D Applications Engineer National Instruments http://www.ni.com/support/